[Biojava-l] Re: Biojava-l digest, Vol 1 #6 - 3 msgs

[Juha Muilu]

David Martin wrote:
> 
-- cut ---
>
> > > These are static properties kept in an external class (or a particular
> > > instance of an AminoAcidTable class. So replacing the
> > > this.getCharAt(i).isCharged()
> > > with
> > > AminoAcidTable.isCharged(this.getCharAt(i))
> > > is the only substantive change.
> >
> > What you say is true enough, but it violates encapsulation.  Instead of
> > the amino acid's state being defined internally, you have to use an
> > external table to look it up.
> 
> If each sequence has an instance of AminoAcidTable as a sequence property
> (much like a nucleotide sequence would have a 'Genetic Code' object) then
> encapsulation is not violated.
>

For me the previous suggestion, having external class is better than
coupling interpretation(s) of an attribute(s) into a same object (here
Sequence object) as suggested by Mark

E.g.. charge of an amino acid depends on many cases. (Please correct me
if I am wrong) You may end up rather complicated class if you try 
to take all possible variations into account
(and add new ones when somebody needs/invite those). This can be done by
delegation, but external utility class as David said, is simpler..

I do not think that this violates encapsulation. It do not change
objects internal state. 

Use of utility classes may make sense with other methods as well. 
Like transcribe(), reveresecomplement() etc...

Juha
> >
-- cut--
>
> 
> ..d
> 
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 |Juha Muilu, Ph.D., EMBL Outstation| Email:  muilu@ebi.ac.uk         |
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